6-31480377-A-G

Variant names:

• chr6-31480377-A-G
• rs2523651
• ENST00000656299.1:n.1000T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656299.1(MICB-DT):​n.1000T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,752 control chromosomes in the GnomAD database, including 30,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (30040 hom., cov: 32)
• Consequence: MICB-DT ENST00000656299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 26 publications found

Genes affected

MICB-DT (HGNC:53632): (MICB divergent transcript)

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656299.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	NR_149132.1		n.1523T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICB-DT	ENST00000656299.1		n.1000T>C		non_coding_transcript_exon	Exon 2 of 2
	MICB-DT	ENST00000665353.2		n.1664T>C		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000718213.1		n.96-10285A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94478 AN: 151634 Hom.: 29989 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.623 AC: 94575 AN: 151752 Hom.: 30040 Cov.: 32 AF XY: 0.627 AC XY: 46498 AN XY: 74184

African (AFR) AF: 0.554 AC: 22872 AN: 41266

American (AMR) AF: 0.682 AC: 10367 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2148 AN: 3466

East Asian (EAS) AF: 0.785 AC: 4049 AN: 5156

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6964 AN: 10552

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42940 AN: 67984

Other (OTH) AF: 0.611 AC: 1287 AN: 2108

Alfa AF: 0.635 Hom.: 112000

Bravo AF: 0.625

Asia WGS AF: 0.696 AC: 2422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2523651; hg19: chr6-31448154;